SAGA HOME PAGE
Sequence Alignment by Genetic Algorithm

PUBLICATIONS
 

SAGA: Sequence Alignment by Genetic Algorithm, C. Notredame, D.G. Higgins, Nucleic Acid Research, Vol. 24, 1515-1524, 1996.
available in [ps][pdf][html].

COFFEE: A New Objective Function For Multiple Sequence Alignmnent. C. Notredame, L. Holme and D.G. Higgins, Bioinformatics, Vol 14 (5) 407-422, 1998
available in [ps][pdf].

SAGA (V 0.95) is available in a TAR file, throught the following link

SAGA v0.95
uncompress and untar the file saga.tar.Z file with the following command:
gzcat SAGA_V0.95.tar.gz | tar xvf -

The Doc folder contains a documentation in PDF format.

SAGA requires a powerful UNIX station to run. It is optimally designed for aligning less than 20 sequences, less than 400 residues long. At present we have no plan to port it on any non-UNIX platform. In a close future, I will support a small FAQ on SAGA including alternative parameter setting for solving different types of problems. Stay in touch and let me know about your needs. E-mail me any trouble you may encounter including SAGA: BUG REPORT in your mail tiltle. I will do my best to fix it :-).

SAGA now also includes the new COFFEE objective function that is based on pairwise alignments consistency. As well as the GA based optimisation, SAGA allows users to do a greedy Tree based optimisation (T-COFFEE) that is much much much faster but less accurate....

I will keep the old version available here for some time.... SAGA v0.93

If you wish to be informed when new updated versions will be made public, please send me an Email cedric.notredame@nimr.mrc.ac.uk including SAGA: NEW VERSION REQUEST and I will put you on my mailing list.

I am more than willing to help anybody who wishes to modify/improve SAGA (i.e. insert new OFs, new mutations ....).